3i04

Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta

OrganismNot specified

UniProt P27989

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha × 2 (P27988) IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 CYANIDE ION × 2 GLYCEROL × 2 COPPER (I) ION × 2 NICKEL (II) ION × 2 ACETATE ION × 2 SODIUM ION × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha × 2 (P27988) IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 CYANIDE ION × 2 GLYCEROL × 2 COPPER (I) ION × 2 NICKEL (II) ION × 2 ACETATE ION × 2 SODIUM ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name DCMB_MOOTH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–673; UniProt 2–674 Author chain B; PDBConstruct 1–673; UniProt 2–674 Author chain C; PDBConstruct 1–673; UniProt 2–674 Author chain D; PDBConstruct 1–673; UniProt 2–674

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

OrganismNot specified

UniProt P27988

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta × 2 (P27989) IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 CYANIDE ION × 2 GLYCEROL × 2 COPPER (I) ION × 2 NICKEL (II) ION × 2 ACETATE ION × 2 SODIUM ION × 2 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta × 2 (P27989) IRON/SULFUR CLUSTER × 5 FE(4)-NI(1)-S(4) CLUSTER × 2 CYANIDE ION × 2 GLYCEROL × 2 COPPER (I) ION × 2 NICKEL (II) ION × 2 ACETATE ION × 2 SODIUM ION × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name DCMA_MOOTH
Isoform —
PDB entities 2
Chains and sequence ranges Author chain M; PDBConstruct 1–728; UniProt 2–729 Author chain N; PDBConstruct 1–728; UniProt 2–729 Author chain O; PDBConstruct 1–728; UniProt 2–729 Author chain P; PDBConstruct 1–728; UniProt 2–729

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3i04
Deposition date deposition_date2009-06-24
Structure title titleCyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster
Keywords keywords;protein-protein complex, Carbon dioxide fixation, Electron transport, Iron, Iron-sulfur, Metal-binding, Nickel, Oxidoreductase, Transport, Transferase, OXIDOREDUCTASE-TRANSFERASE COMPLEX ;; OXIDOREDUCTASE/TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3i04__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3i04__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3i04__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)51.63 Å
Rg (electron density)52.43 Å
Total Rg52.11 Å
Atom count21736
Residues2802
Excluded volume389260 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3i04__assembly_1__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3i04__assembly_2__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3i04a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.2 — Carbon monoxide dehydrogenase
Domain ID domain_idd3i04b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.2 — Carbon monoxide dehydrogenase
Domain ID domain_idd3i04c_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.2 — Carbon monoxide dehydrogenase
Domain ID domain_idd3i04d_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.2 — Carbon monoxide dehydrogenase
Domain ID domain_idd3i04m_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.3 — Acetyl-CoA synthase
Domain ID domain_idd3i04n_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.3 — Acetyl-CoA synthase
Domain ID domain_idd3i04o_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.3 — Acetyl-CoA synthase
Domain ID domain_idd3i04p_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.26 — Prismane protein-like
Superfamily Superfamily superfamilye.26.1 — Prismane protein-like
Family Family familye.26.1.3 — Acetyl-CoA synthase

CATH v4.4 (32 domains)

Domain ID domain_id3i04A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3i04A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04B01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3i04B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04B03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04C01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3i04C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04C03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04D01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3i04D02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04D03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04M01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1
Domain ID domain_id3i04M02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04M03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Domain ID domain_id3i04M04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4
Domain ID domain_id3i04M05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Domain ID domain_id3i04N01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1
Domain ID domain_id3i04N02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04N03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Domain ID domain_id3i04N04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4
Domain ID domain_id3i04N05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Domain ID domain_id3i04O01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1
Domain ID domain_id3i04O02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04O03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Domain ID domain_id3i04O04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4
Domain ID domain_id3i04O05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Domain ID domain_id3i04P01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1
Domain ID domain_id3i04P02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2030 —
Domain ID domain_id3i04P03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3
Domain ID domain_id3i04P04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4
Domain ID domain_id3i04P05
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
Homologous superfamily homologous superfamily10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5
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7. Citations (1)